I'm curious as to why you are looping over the views in the first place. Maybe we could arrive at a vectorized solution, which is often but not always simpler and faster.
Michael On Wed, Apr 5, 2017 at 8:13 PM, Pariksheet Nanda <pariksheet.na...@uconn.edu> wrote: > Hi bioconductor devs, > > The BSgenomeViews class has been very useful in efficiently propagating > metadata for running Biostring operations. I noticed something unexpected > when iterating over views - it seems to return the Biostrings object > instead of a single length Views object, and thus loses the associated view > metadata. Is this intentional? Below is some example code, the output and > sessionInfo(). Yes, I also confirmed this happens in the development > version of R / bioconductor 3.5. > > On a side note, for unit testing it's been difficult to mock a BSgenome > object due to the link to physical files, and as a workaround I use a > small, arbitrary BSgenome package. Can one construct a BSgenome from its > package bundled extdata? The man page examples use packaged genomes. > > Code to reproduce the issue: > > ---------------------------------------------------------------------- > library(BSgenome) > genome <- getBSgenome("BSgenome.Hsapiens.UCSC.hg19") > gr <- GRanges(c("chr1:25001-28000", "chr2:30001-31000")) > views <- Views(genome, gr) > views > lapply(views, class) > ---------------------------------------------------------------------- > > Result: > > ---------------------------------------------------------------------- >> views > BSgenomeViews object with 2 views and 0 metadata columns: > seqnames ranges strand dna > <Rle> <IRanges> <Rle> <DNAStringSet> > [1] chr1 [25001, 28000] * [GCTTCAGCCT...TTATTTATTG] > [2] chr2 [30001, 31000] * [GACCCTCCTG...AGCAGGTGGT] > ------- > seqinfo: 93 sequences (1 circular) from hg19 genome >> lapply(views, class) > [[1]] > [1] "DNAString" > attr(,"package") > [1] "Biostrings" > > [[2]] > [1] "DNAString" > attr(,"package") > [1] "Biostrings" > >> > ---------------------------------------------------------------------- > > Tested against these configurations: > 1) R 3.3.2 + BSgenome 1.42.0 (stable bioconductor 3.4) > 2) R 2017-04-05 installed via llnl/spack + BSgenome 1.43.7 (devel > bioconductor 3.5) > > sessionInfo for configuration #2 above: > ---------------------------------------------------------------------- >> sessionInfo() > R Under development (unstable) (2017-04-05 r72488) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 16.04.2 LTS > > Matrix products: default > BLAS: > /share/apps/spack/opt/spack/linux-ubuntu16-x86_64/gcc-5.4.0/r-2017-04-05-4tkzhsu6sdpwmlvnv275jf6x766gwnpy/rlib/R/lib/libRblas.so > LAPACK: > /share/apps/spack/opt/spack/linux-ubuntu16-x86_64/gcc-5.4.0/r-2017-04-05-4tkzhsu6sdpwmlvnv275jf6x766gwnpy/rlib/R/lib/libRlapack.so > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats4 parallel stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.43.7 > [3] rtracklayer_1.35.10 Biostrings_2.43.7 > [5] XVector_0.15.2 GenomicRanges_1.27.23 > [7] GenomeInfoDb_1.11.10 IRanges_2.9.19 > [9] S4Vectors_0.13.15 BiocGenerics_0.21.3 > > loaded via a namespace (and not attached): > [1] zlibbioc_1.21.0 GenomicAlignments_1.11.12 > [3] BiocParallel_1.9.5 lattice_0.20-35 > [5] tools_3.5.0 SummarizedExperiment_1.5.7 > [7] grid_3.5.0 Biobase_2.35.1 > [9] matrixStats_0.52.1 Matrix_1.2-9 > [11] GenomeInfoDbData_0.99.0 bitops_1.0-6 > [13] RCurl_1.95-4.8 DelayedArray_0.1.7 > [15] compiler_3.5.0 Rsamtools_1.27.15 > [17] XML_3.98-1.6 >> BiocInstaller::biocValid() > [1] TRUE >> > > --- > Pariksheet Nanda > PhD Candidate in Genetics and Genomics > System Administrator, Storrs HPC Cluster > University of Connecticut > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel